Table1_Identification of Potential Prognostic Biomarkers Associated With Macrophage M2 Infiltration in Gastric Cancer.DOC

Gastric cancer is a common cancer afflicting people worldwide. Although incremental progress has been achieved in gastric cancer research, the molecular mechanisms underlying remain unclear. In this study, we conducted bioinformatics methods to identify prognostic marker genes associated with gastric cancer progression. Three hundred and twenty-seven overlapping DEGs were identified from three GEO microarray datasets. Functional enrichment analysis revealed that these DEGs are involved in extracellular matrix organization, tissue development, extracellular matrix–receptor interaction, ECM-receptor interaction, PI3K-Akt signaling pathway, focal adhesion, and protein digestion and absorption. A protein–protein interaction network (PPI) was constructed for the DEGs in which 25 hub genes were obtained. Furthermore, the turquoise module was identified to be significantly positively coexpressed with macrophage M2 infiltration by weighted gene coexpression network analysis (WGCNA). Hub genes of COL1A1, COL4A1, COL12A1, and PDGFRB were overlapped in both PPI hub gene list and the turquoise module with significant association with the prognosis in gastric cancer. Moreover, functional analysis demonstrated that these hub genes play pivotal roles in cancer cell proliferation and invasion. The investigation of the gene markers can help deepen our understanding of the molecular mechanisms of gastric cancer. In addition, these genes may serve as potential prognostic biomarkers for gastric cancer diagnosis.</p

Genetic diversity of <i>Polyporus umbellatus</i> collected from different provinces^*.

*<p>Forty-two samples were sequenced in this study (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058807#pone.0058807.s001" target="_blank">Table S1</a>). The genetic parameters of nucleotide diversity were estimated by DnaSP software (version 5.10.01). The “polymorphic sites” include both informative sites and singleton sites.</p

Genetic Diversity and Evolution of Chinese Traditional Medicinal Fungus <em>Polyporus umbellatus</em> (Polyporales, Basidiomycota)

<div><p>Background</p><p><i>Polyporus umbellatus</i> is an important medicinal fungus distributed throughout most area of China. Its wide distribution may have resulted in substantial intraspecific genetic diversity for the fungus, potentially creating variation in its medical value. To date, we know little about the intraspecific genetic diversity of <i>P. umbellatus</i>.</p> <p>Methodology/Principal Findings</p><p>The objective of this research was to assess genetic differences of <i>P. umbellatus</i> from geographically diverse regions of China based on nrDNA ITS and 28S rRNA (LSU, large subunit) sequences. Significant sequence variations in the ITS and LSU sequences were detected. All sclerotial samples were clustered into four clades based on phylogenetic analysis of ITS, LSU and a combined data set of both regions. Heterogeneity of ITS and LSU sequences was detected in 5 and 7 samples respectively. All clone sequences clustered into the same clade except for one LSU clone sequences (from Henan province) which clustered into two clades (Clade I and Clade II). Significant genetic divergence in <i>P. umbellatus</i> was observed and the genetic diversification was greater among sclerotial samples from Shaanxi, Henan and Gansu provinces than among other provinces. Polymorphism of ITS and LSU sequences indicated that in China, <i>P. umbellatus</i> may spread from a center (Shaanxi, Henan and Gansu province) to other regions.</p> <p>Conclusions/Significance</p><p>We found sclerotial samples of <i>P. umbellatus</i> contained levels of intraspecific genetic diversity. These findings suggested that <i>P. umbellatus</i> populations in Shaanxi, Henan and Gansu are important resources of genetic diversity and should be conserved accordingly.</p> </div

PCR-SSCP results of ITS and LSU sequences of <i>Polyporus umbellatus</i>.

a<p>Numbers outside parentheses are parsimony informative sites, inside parentheses are singleton variable sites.</p

Pairwise population difference for ITS and LSU sequences of <i>Polyporus umbellatus</i> sclerotia.

<p>Above diagonal: Average number of pairwise differences between populations (PiXY); Diagonal elements: Average number of pairwise differences within population (PiX); Below diagonal: Corrected average pairwise difference (PiXY−(PiX+PiY)/2); P values of PXY are indicated (* p<0.05; **p<0.01).</p

AMOVA for grouping of sclerotial populations using F-statistics based on ITS and LSU sequences.

<p>Notes: <i>F</i>_SC estimates the variation among populations relative to a regional grouping of populations. <i>F</i>_ST estimates the proportions of genetic variation within populations relative to the genetic variation for the whole samples. <i>F</i>_CT estimates the proportion of genetic variation among groups of populations relative to the whole species. <i>F</i>_CT values that are statistically different are indicted. The P values are indicated as * <0.05, ** <0.01.</p

Phylogenetic analyses of 42 <i>Polyporus umbellatus</i> sclerotia based on the combined data set of nrDNA ITS and LSU (28S rRNA).

<p>Bootstrap values from minimum evolution, maximum parsimony and maximum likelihood higher than 50% are shown at the nodes. The representative sclerotial pictures of each combined haplotypes are shown aside. Arabic numbers (1–7) indicate ITS haplotypes and capital letters (A–G) indicate LSU haplotypes. Sample codes: The capital letters after ZL indicate the provinces names: ShX “Shaanxi Province, SX “Shanxi Province”, HB “Hebei Province”, HN “Henan Province”, SC “Sichuan Province”, GS “Gansu Province”, QH “Qinghai Province”, YN “Yunnan Province”, JL “Jilin Province”, LN “Liaoning Province”, HLJ “Heilongjiang Province”, BJ “Beijing”. Symbols marked at the side of sclerotial images refer to sclerotial morphotypes: ▵ “<i>Zhu Shi Ling</i>”, ??? “<i>Ji Shi Ling</i>”. Arabic numbers after province name indicate the sample number from same province (also see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058807#pone.0058807.s001" target="_blank">Table S1</a>).</p

Phylogenetic analyses of ITS and LSU clones and their original sequences from direct sequencing.

<p>Bootstrap values from minimum evolution and maximum parsimony higher than 50% are shown at the nodes. 2A. Phylogenetic analyses based on ITS sequences of 31 clones and their original sequences from direct sequencing. <i>Polyporus squamosus</i> FR686579 was used as outgroup. The Arabic number after the clone represents clone number. 2B. Phylogenetic analyses based on LSU sequences of 49 clones and their original sequences from direct sequencing. <i>Boletopsis leucomelaena</i> DQ154112 was used as outgroup. “▴” indicates original sequence of ZL-HN-5. “•” indicates clones of ZL-HN-5. Samples represent different provinces (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058807#pone-0058807-g001" target="_blank">Fig. 1</a> for legend).</p

Interactions between residue S/A138 and NHR for N43D and N43D/S138A mutant.

<p>a and b represent interactions between S/A138 and NHR residues in N43D single mutant and N43D/S138A double mutant.</p

Structures of N43D mutant (blue) and N43D/S138A double mutant (white).

<p>Structures of N43D mutant (blue) and N43D/S138A double mutant (white).</p